The NuA4 complex promotes Translesion Synthesis (TLS) - mediated DNA damage tolerance
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE66176 | GEO | 2015/02/21
SECONDARY ACCESSION(S): PRJNA276018
REPOSITORIES: GEO
Similar Datasets
Project description:DNA lesions can block a replication fork, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, DNA damage tolerance (DDT) pathways become engaged, allowing the replisome to bypass the lesion and complete S phase in the presence of unrepaired damage. Here we demonstrate a newly identified role for NuA4, including complex components Esa1 and Yng2, on the Translesion Synthesis (TLS) branch of DDT. Moreover, Our data suggest that NuA4 functionality within the tolerance pathway is likely direct as genome-wide transcriptional analysis with esa1-L254P mutants showed little changes in the expression of TLS factors compared to wild type during MMS treatment. When Yng2 expression is restricted to G2/M, cell viability and mutagenesis rates are restored to the levels measured when only the error-free branch of DDT is disrupted, indicating that the critical role of NuA4 in TLS functions in G2, after chromosomal replication is complete. Lastly, disruption of HTZ1, the Saccharomyces cerevisiae histone variant H2A.Z and target of NuA4, exhibits mutagenic rates of reversion that are comparable to the levels measured with NuA4 complex mutants, esa1-L254P and yng2M-NM-^T. The esa1-L254P strain was compared to wild type through a series of microarrays utilizing dye swaps with and without treatment of MMS. These included synchronized cells in G1 and S phase through alpha factor treatment. Four unique microarrays were performed each with dye swaps, comparing wild type to esa1-L254P in G1 and S phase with and without treatment with MMS. As a set of controls, four microarrays were performed comparing identical strains with and without MMS in G1 or S phase.
2015-02-21 | E-GEOD-66176 | biostudies-arrayexpress
Project description:Many DNA tumor viruses inhibit or repurpose host DNA repair pathways to evade viral defense mechanisms or promote their own replication. High risk genus α human papillomaviruses (α-HPVs) express two versatile oncogenes (α-HPV E6 and E7) that use both approaches simultaneously. To identify new interactions with DNA repair pathways, we conducted a computational analysis of gene expression in cervical cancer (CaCx) transcriptomic datasets and identified a frequent upregulation of translesion synthesis (TLS) genes. TLS polymerase genes, particularly the gene for POLη (POLH), did not follow this pattern. Characterization of α-HPV oncogene expressing cell lines and premalignant cervical tissue confirm these data. They also show that the increased TLS protein abundance come in response to nucleoside depletion. Primary and transformed cell lines to demonstrate that α-HPV E6 blocks POLη induction by degrading p53. Lack of POLη dooms the pathway, preventing it from facilitating tolerance of replication stress. Failed TLS results in replication fork stalling and collapse into deleterious double strand breaks in the DNA (DSBs). Consequently, cellular genome fidelity decreases in a manner consistent with the mutations that accumulate during CaCx progression. Alterations in TLS are determinants for the efficacy of the chemotherapeutics most often used to treat CaCx (cisplatin and carboplatin). Exogenous expression of POLη protected CaCx cells from cisplatin-associated toxicity/damage, effectively stabilizing their genome. TLS polymerase expression is also a prognostic factor in CaCx. Analysis of the cancer genome atlas database (TCGA) shows increased expression of these genes correlated with over a decade shorter median survival.
2020-05-01 | GSE145976 | GEO
Project description:Histone post-translational modifications (PTMs) are critical for processes such as transcription. The more notable among these are the non-acetyl histone lysine acylation modifications such as crotonylation, butyrylation and succinylation. However, the biological relevance of these PTMs is not fully understood because their regulation is largely unknown. Here, we set out to investigate whether the main histone acetyltransferases in budding yeast, Gcn5 and Esa1, possess crotonyltransferase activity. In vitro studies revealed that the Gcn5-Ada2-Ada3 (ADA) and Esa1-Yng2-Epl1 (Piccolo NuA4) histone acetyltransferase complexes have the capacity to crotonylate histones. Mass spectrometry analysis revealed that ADA and Piccolo NuA4 crotonylate lysines in the N-terminal tails of histone H3 and H4, respectively. Functionally, we show that crotonylation selectively affects gene transcription in vivo in a manner dependent on Gcn5 and Esa1. Thus, we identify the Gcn5- and Esa1-containing ADA and Piccolo NuA4 complexes as bona fide crotonyltransferases that promote crotonylation-dependent transcription.
2019-11-06 | PXD015488 | Pride
Project description:The NuA4 complex promotes Translesion Synthesis (TLS) - mediated DNA damage tolerance
| PRJNA276018 | ENA
Project description:Enzymes that modify and remodel chromatin are subunits in broadly conserved macromolecular complexes. One key chromatin modification is the dynamic acetylation of histones by opposing activities of acetyltransferase and deacetylase complexes. Among the acetyltransferases, the NuA4 complex containing Tip60 or its Saccharomyces cerevisiae ortholog, Esa1, is of particular significance because of its roles in crucial genomic processes including DNA damage repair and transcription. The catalytic subunit Esa1 is essential, as are five non-catalytic NuA4 subunits. We found that of these non-catalytic subunits, only deletion of Enhancer of polycomb (Epl1) can be bypassed by loss of a major deacetylase complex. This is a property shared by Esa1. Non-catalytic complex subunits are often critical for complex assembly, stability, genomic targeting, substrate specificity and regulation. Understanding the essential cellular role of Epl1 has been limited, a limitation now overcome by the discovery of its bypass suppression. Here, we present the first comprehensive in vivo study of Epl1 upon complete cellular loss of Epl1 using the powerful tool of suppression combined with transcriptional and mutational analyses. Our results highlight functional parallels between Epl1 and Esa1 and further illustrate that the structural role of Epl1 is important for promotion of Esa1 activity. This conclusion is strengthened by our dissection of Epl1 domains required in vivo for interaction with specific NuA4 subunits, histone acetylation, and chromatin targeting. These results provide new insights for the conserved, essential nature of Epl1 and its homologs among organisms, such as EPC1/2 in humans, which is frequently altered in cancers.
2017-01-19 | GSE92774 | GEO
Project description:Mutations in DNA damage response (DDR) factors are associated with human infertility, which affects up to 15% of the population. It remains unclear if the role of DDR is solely in meiosis. One pathway implicated in human fertility is DNA translesion synthesis (TLS), which allows replication impediments to be bypassed. We find that TLS is essential for pre-meiotic germ cell development in the embryo. Loss of the central TLS component, REV1, significantly inhibits the induction of human PGC-like cells (hPGCLCs). This is recapitulated in mice, where deficiencies in TLS initiation (Rev1-/- or PcnaK164R/K164R) or extension (Rev7-/-) result in a >150-fold reduction in the number of primordial germ cells (PGCs) and complete sterility. In contrast, the absence of TLS does not impact the growth, function, or homeostasis of somatic tissues. Surprisingly, we find a complete failure in both DNA demethylation, a critical step in germline epigenetic reprogramming, and in activation of the germ cell transcriptional program. Our findings show that for normal fertility, DNA repair is required not only for meiotic recombination but for completion of DNA demethylation and the progression of PGC development.
2024-04-15 | GSE253991 | GEO
Project description:The tolerance pathway allows bypassing deleterious lesions that block replicative DNA polymerases. In eukaryotes tolerance is controlled by ubiquitylation of the DNA replication factor PCNA4. Here, we show that PCNAK164-ubiquitin proteases (PCNA-DUBs) Ubp10 and Ubp12 localise to replication forks. In particular, the main PCNA-DUB, Ubp10, associates primarily to nascent lagging strands. We also found that cells deficient for PCNA deubiquitylation show both increased interaction of TLS polymerase ζ-associated Rev1 with lagging strands and Rad52-dependent template switching events. This evidence reveals a fork-coupled layer of DDT regulation allowing strand-specific pathway choices.
2019-10-29 | GSE90157 | GEO
Project description:The transcriptional co-activators Mediator and two histone acetyltransferase (HAT) complexes, NuA4 and SAGA, play global roles in transcriptional activation. Here we explore the relative contributions of these factors to RNA polymerase II association at specific genes and gene classes by rapid nuclear depletion of key complex subunits. We show that the NuA4 HAT Esa1 differentially affects certain groups of genes, whereas the SAGA HAT Gcn5 has a weaker but more uniform effect. Relative dependence on Esa1 and Tra1, a shared component of NuA4 and SAGA, distinguishes two large groups of co-regulated growth-promoting genes. In contrast, we show that the activity of Mediator is particularly important at a separate, small set of highly transcribed TATA box-containing genes. Our analysis indicates that at least three distinct combinations of co-activator deployment are used to generate moderate or high transcription levels, and suggests that each may be associated with distinct forms of regulation.
2018-08-15 | GSE109235 | GEO
Project description:ESA1 (essential SAS-family acetyltransferase) is the only known yeast histone acetyltransferase (HAT) required for cell viability. It is a member of the MYST (MOZ, YBF2/SAS3, SAS2, Tip60) family of HAT proteins and contains a conserved acetyltransferase domain in addition to a chromodomain. While ESA1’s HAT activity is important in processes such as deoxyribonucleic acid (DNA) repair, acetylation is likely not its essential function. Our lab has shown that mutants with a single point mutation in the active site cysteine are still viable even though their acetyltransferase abilities are abolished. Furthermore, chromatin immunoprecipitation assays have shown ESA1 distributed evenly along the length of chromatin, not localized to specific promoters as would be expected from a HAT protein involved in transcriptional regulation. As is the case for other HAT proteins, ESA1’s acetyltransferase activity is significant, but in processes such as DNA replication, DNA repair and cell cycle progression. The aim of this project is to determine the essential function of ESA1 - the catalytic subunit of the yeast HAT complex, NuA4 (nucleosome acetyltransferase of H4) – using a bypass suppression screen to identify suppressors of ESA1. It is proposed that suppressing mutations will alter a gene involved in the process that is the essential function of ESA1. Thus, identifying a suppressor that can bypass the need for ESA1 may provide insight into its essential function. Since ESA1 is an essential gene, a haploid esa1∆ strain in which wild-type ESA1 is provided on a centromeric plasmid was utilized. The bypass suppression screen resulted in suppressors of ESA1 that allowed esa1∆ cells to be viable even in the absence of the essential gene. These second site suppressors (sup-) of ESA1 each show the Mendelian segregation pattern of the suppressing gene and ESA1 in 2:2 ratios, implying they are single genes unlinked to ESA1. Microarray and nuclear morphology studies show abnormal gene expression and morphology of the esa1- sup- cells, further implicating the suppressing mutation in DNA repair and replication processes. Investigating ESA1’s essential role and a probable conservation of function across species can provide a deeper understanding of the capabilities of HAT complexes. Keywords: Comparison of strains lacking essential ESA1 gene to those containing an ESA1 bypass suppressor.
2007-12-12 | GSE9840 | GEO
Project description:ESA1 (essential SAS-family acetyltransferase) is the only known yeast histone acetyltransferase (HAT) required for cell viability. It is a member of the MYST (MOZ, YBF2/SAS3, SAS2, Tip60) family of HAT proteins and contains a conserved acetyltransferase domain in addition to a chromodomain. While ESA1âs HAT activity is important in processes such as deoxyribonucleic acid (DNA) repair, acetylation is likely not its essential function. Our lab has shown that mutants with a single point mutation in the active site cysteine are still viable even though their acetyltransferase abilities are abolished. Furthermore, chromatin immunoprecipitation assays have shown ESA1 distributed evenly along the length of chromatin, not localized to specific promoters as would be expected from a HAT protein involved in transcriptional regulation. As is the case for other HAT proteins, ESA1âs acetyltransferase activity is significant, but in processes such as DNA replication, DNA repair and cell cycle progression. The aim of this project is to determine the essential function of ESA1 - the catalytic subunit of the yeast HAT complex, NuA4 (nucleosome acetyltransferase of H4) â using a bypass suppression screen to identify suppressors of ESA1. It is proposed that suppressing mutations will alter a gene involved in the process that is the essential function of ESA1. Thus, identifying a suppressor that can bypass the need for ESA1 may provide insight into its essential function. Since ESA1 is an essential gene, a haploid esa1â strain in which wild-type ESA1 is provided on a centromeric plasmid was utilized. The bypass suppression screen resulted in suppressors of ESA1 that allowed esa1â cells to be viable even in the absence of the essential gene. These second site suppressors (sup-) of ESA1 each show the Mendelian segregation pattern of the suppressing gene and ESA1 in 2:2 ratios, implying they are single genes unlinked to ESA1. Microarray and nuclear morphology studies show abnormal gene expression and morphology of the esa1ï sup- cells, further implicating the suppressing mutation in DNA repair and replication processes. Investigating ESA1âs essential role and a probable conservation of function across species can provide a deeper understanding of the capabilities of HAT complexes. Experiment Overall Design: Eight samples were analyzed. The only variables are the ESA1 and SUP2 genes. WT (ESA1 SUP2), 2 replicates. Single mutant (ESA1 sup2-), 3 replicates. Double mutant (esa1 sup2-), 3 replicates.
2008-06-16 | E-GEOD-9840 | biostudies-arrayexpress